rs525028

Variant names:

• chr11-116834800-G-A
• rs525028

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.505 in 151,862 control chromosomes in the GnomAD database, including 23,112 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (23112 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76698 AN: 151744 Hom.: 23122 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.528

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.505 AC: 76686 AN: 151862 Hom.: 23112 Cov.: 30 AF XY: 0.497 AC XY: 36876 AN XY: 74202

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.522

Alfa AF: 0.532 Hom.: 3584

Bravo AF: 0.485

Asia WGS AF: 0.303 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs525028; hg19: chr11-116705516;